Release 2.3.1 #238

jonasscheid · 2024-03-25T12:41:03Z

Small release:

Merge template update 2.13.1
Remove Channel.view statement that has accidently sneaked its way into the previous release
Add check for protein map to prevent failure if no information is available (@christopher-mohr)

PR checklist

github-actions · 2024-03-25T12:42:47Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 0282263

+| ✅ 202 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.3.1
schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

files_unchanged - File ignored due to lint config: assets/nf-core-epitopeprediction_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-epitopeprediction_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-epitopeprediction_logo_dark.png

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-epitopeprediction_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-epitopeprediction_logo_light.png
files_exist - File found: docs/images/nf-core-epitopeprediction_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-epitopeprediction_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowEpitopeprediction.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.genome_reference= grch37
nextflow_config - Config default value correct: params.max_peptide_length= 11
nextflow_config - Config default value correct: params.min_peptide_length= 8
nextflow_config - Config default value correct: params.max_peptide_length_class2= 16
nextflow_config - Config default value correct: params.min_peptide_length_class2= 15
nextflow_config - Config default value correct: params.tools= syfpeithi
nextflow_config - Config default value correct: params.split_by_variants_size= 0
nextflow_config - Config default value correct: params.split_by_variants_distance= 110000
nextflow_config - Config default value correct: params.peptides_split_maxchunks= 100
nextflow_config - Config default value correct: params.peptides_split_minchunksize= 5000
nextflow_config - Config default value correct: params.netmhc_system= linux
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (124 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: ci-external.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - EPYTOPE_CHECK_REQUESTED_MODELS found in conf/modules.config and Nextflow scripts.
modules_config - EPYTOPE_CHECK_REQUESTED_MODELS_PEP found in conf/modules.config and Nextflow scripts.
modules_config - EPYTOPE_GENERATE_PEPTIDES found in conf/modules.config and Nextflow scripts.
modules_config - SPLIT_PEPTIDES_PEPTIDES found in conf/modules.config and Nextflow scripts.
modules_config - SPLIT_PEPTIDES_PROTEIN found in conf/modules.config and Nextflow scripts.
modules_config - EPYTOPE_PEPTIDE_PREDICTION_PROTEIN found in conf/modules.config and Nextflow scripts.
modules_config - EPYTOPE_PEPTIDE_PREDICTION_PEP found in conf/modules.config and Nextflow scripts.
modules_config - EPYTOPE_PEPTIDE_PREDICTION_VAR found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_JSON_SINGLE found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_JSON_MULTI found in conf/modules.config and Nextflow scripts.
modules_config - CAT_TSV found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTA found in conf/modules.config and Nextflow scripts.
modules_config - CSVTK_CONCAT found in conf/modules.config and Nextflow scripts.
modules_config - GET_PREDICTION_VERSIONS found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP_VCF found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_JSON found in conf/modules.config and Nextflow scripts.
modules_config - EPYTOPE_SHOW_SUPPORTED_MODELS found in conf/modules.config and Nextflow scripts.
modules_config - VARIANT_SPLIT found in conf/modules.config and Nextflow scripts.
modules_config - SNPSIFT_SPLIT found in conf/modules.config and Nextflow scripts.
modules_config - SPLIT_PEPTIDES found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-05-16 07:53:27

christopher-mohr

Have to check what's going on with biomart again...

CHANGELOG.md

Add stubs to all local modules

christopher-mohr · 2024-03-28T12:32:14Z

Have to check what's going on with biomart again...

It just seems to randomly fail within CI (now again). Last time I could not reproduce it on GitPod...

CHANGELOG.md

christopher-mohr · 2024-05-13T06:33:31Z

@jonasscheid What's the status here?

jonasscheid · 2024-05-13T11:42:40Z

I thought we are currently stuck because of some random ci tests failing. I'll do the template merge this week and look at again

christopher-mohr · 2024-05-14T15:19:57Z

I thought we are currently stuck because of some random ci tests failing. I'll do the template merge this week and look at again

I think this was just the BioMart connection issue that happens from time to time. The test profile also runs fine on GitPod. I can do the template merge later today or tomorrow morning then we see if the problem still exists (on CI).

jonasscheid · 2024-05-15T05:35:40Z

Great, thank you! 🙏

… into merge-template-update-2-14-1

Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com>

…istopher-mohr/nf-core-epitopeprediction into merge-template-update-2-14-1

…-14-1 Merge template updates up to 2.14.1

christopher-mohr

LGTM

mapo9

lgtm

workflows/epitopeprediction.nf

nf-core-bot and others added 4 commits February 29, 2024 16:09

Template update for nf-core/tools version 2.13.1

377cd7f

remove view

e2b2e7a

prepare for release

e253f8b

Merge pull request #237 from jonasscheid/merge-template

3cee77a

christopher-mohr reviewed Mar 26, 2024

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jonasscheid added 3 commits March 27, 2024 22:10

add stub to all local modules

a1e9af9

fix changelog date

16329c4

revert args to argument

63e13c8

jonasscheid mentioned this pull request Mar 28, 2024

Add stubs to all local modules #239

Merged

11 tasks

Merge pull request #239 from jonasscheid/merge-template

81fba13

Add stubs to all local modules

christopher-mohr reviewed Mar 28, 2024

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nf-core-bot added 2 commits May 8, 2024 13:58

Template update for nf-core/tools version 2.14.0

fe1de34

Template update for nf-core/tools version 2.14.1

ae1fb38

christopher-mohr and others added 10 commits May 15, 2024 06:31

Merge branch 'TEMPLATE' of https://github.com/nf-core/epitopeprediction…

ee75ad3

… into merge-template-update-2-14-1

remove dumpsoftwareversions

e7345fc

remove fastqc from modules.json

9170272

update CHANGELOG

e2cf136

update all test config input paths

673a805

Update CHANGELOG.md

fe02f4d

Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com>

add check to epaa, update CHANGELOG

f66e334

Merge branch 'merge-template-update-2-14-1' of https://github.com/chr…

93d6500

…istopher-mohr/nf-core-epitopeprediction into merge-template-update-2-14-1

add warning if protein mapping not available

16d714a

Merge pull request #243 from christopher-mohr/merge-template-update-2…

0282263

…-14-1 Merge template updates up to 2.14.1

christopher-mohr approved these changes May 17, 2024

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mapo9 approved these changes May 17, 2024

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jonasscheid merged commit cfbfeb5 into master May 17, 2024
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Release 2.3.1 #238

Release 2.3.1 #238

jonasscheid commented Mar 25, 2024 •

edited

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github-actions bot commented Mar 25, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

christopher-mohr left a comment

christopher-mohr commented Mar 28, 2024

christopher-mohr commented May 13, 2024

jonasscheid commented May 13, 2024

christopher-mohr commented May 14, 2024

jonasscheid commented May 15, 2024

christopher-mohr left a comment

mapo9 left a comment

Release 2.3.1 #238

Release 2.3.1 #238

Conversation

jonasscheid commented Mar 25, 2024 • edited Loading

PR checklist

github-actions bot commented Mar 25, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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christopher-mohr commented Mar 28, 2024

christopher-mohr commented May 13, 2024

jonasscheid commented May 13, 2024

christopher-mohr commented May 14, 2024

jonasscheid commented May 15, 2024

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jonasscheid commented Mar 25, 2024 •

edited

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github-actions bot commented Mar 25, 2024 •

edited

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`nf-core lint` overall result: Passed ✅ ⚠️